The development of an accurate gene map is a primary goal of cytogenetic studies in any organism. Chromosomal and band localization of genes in animal genomes can elucidate the evolution of genome organization. Moreover, knowledge of genome organization facilitates integration with human medical research of genetic studies of animal models such as canine behavioral traits and genetic diseases. However, the karyotype of the 78 dog chromosomes is incompletely standardized, and to date no autosomal localization by FISH of a canine gene or anonymous sequence has been reported. We analyzed pre-harvest treatment with EtBr and/or BrdU for dog lymphocyte chromosomes. High quality metaphases for FISH were obtained with BrdU, and this treatment also allowed for simultaneous fluorescent banding under UV light with FISH. Conditions for FISH were optimized using both canine genomic probes (phage and plasmids) and cross-species hybridization with human YACs. The X-linked F8 and F9 genes, the MHC locus (DLA) and the immunoglobulin heavy chain locus have been mapped in the dog. Mapping of canine X-linked SCID has also been accomplished. Further studies are focused on inclusion of cat chromosomes, more tractable for karyotypic analysis, and mapping of the locus for canine narcolepsy, which has been extensively studied and occurs as a simple dominant trait in large pedigrees of dogs studied by our Stanford University Medical Center collaborator, Emmanuel Mignot.